Biology subjects

Follows, M.

Publications and source records attributed to Follows, M..

4 recordsLinked to original sources

bioRxiv2026

Invariant scaling of the Species Abundance Distribution in observed and simulated marine plankton communities

Marine plankton are functionally diverse and span over five orders of magnitude in diameter, with important consequences for marine biogeochemical cycles. Marine ecosystem simulations are beginning to resolve this diversity; however, major uncertainties persist regarding the structure and function of planktonic ecosystems. Here we diagnosed plankton Species Abundance Distributions (SADs) in large-scale surveys and in a global, mechanistic plankton community simulation. The fitted slopes of the SADs vary by less than 10% across latitude, season, and biome in both observations and the simulation. Fitting parametric SADs further reveals spatial structure in the shape and functional form of the SAD aligned with established biogeographic provinces. Together, these results demonstrate a largely invariant structure of marine plankton communities that persists despite strong environmental gradients and taxonomic turnover. These findings suggest that the emergent shape and scaling of plankton SADs reflect fundamental constraints on community assembly and provide a compact quantitative diagnostic for planktonic ecosystem structure.

ecology↗

bioRxiv2026

Estimating absolute microbial abundances from metabarcoding anchored to cytometry data

Over the past decades, metabarcoding and automated cell-counting approaches have greatly advanced our understanding of marine microbial communities. Metabarcoding provides high taxonomic resolution and comprehensive community characterization, typically as relative gene abundances, whereas flow cytometry provides absolute cell abundances but lower taxonomic coverage. Here, we assess whether concurrent flow-cytometry observations can calibrate metabarcoding data to derive absolute gene abundances across four basin-scale Atlantic and Pacific Ocean transects. We first show that flow-cytometry-anchored calibration reproduces absolute abundances of Prochlorococcus and Synechococcus with performance comparable (R2 = 0.87) to internal DNA standard-based quantification. For datasets lacking internal standards, the choice of cytometric "anchor" species introduces systematic offsets in absolute abundance estimates, although spatial patterns remain robust. These offsets may reflect underestimation of cytometric counts or variation in rRNA gene copy numbers among actively dividing cells. We therefore recommend the use of multiple anchors where possible to diagnose systematic uncertainty. Applying this framework, we derive absolute gene concentrations for diverse plankton taxa from compositional metabarcoding data. For taxa with known rRNA gene copy numbers, calibration further enables estimation of absolute cell concentrations. We also resolve ecotype-level absolute abundances of Prochlorococcus along a longitudinal temperature gradient, revealing ecological patterns not apparent from compositional or cytometric data alone. Our results demonstrate that calibrated metabarcoding provides a practical quantitative bridge between molecular and cytometric observations, yielding high taxonomic resolution together with absolute gene concentrations and quantified uncertainties.

ecology↗

bioRxiv2025

Four Potential Mechanisms Underlying Phytoplankton-Bacteria Interactions Assessed Using Experiments and Models

Phytoplankton growth and death depend on interactions with heterotrophic bacteria, yet the underlying mechanisms remain mostly unclear. We ask whether mathematical models explicitly representing four putative mechanisms of interaction (overflow metabolism, mixotrophy, exoenzymes and ROS detoxification) can recapitulate laboratory co-cultures between Prochlorococcus and 8 heterotrophic bacteria, ranging from synergism to antagonism. Two fundamentally distinct modes of interaction emerge from the models: i) Organic carbon and nitrogen recycling through exoenzymes or overflow metabolism, where high biomass of both organisms leads to more productive systems and more recalcitrant organic matter. ii) Detoxification of ROS, where a small number of "exploited" heterotrophs are sufficient to support Prochlorococcus survival. Cross feeding is likely more common in laboratory co-cultures, and most models cannot reproduce total inhibition of Prochlorococcus, suggesting additional mechanisms such as allelopathy. Key model parameters determining co-culture outcome are related to cell death and biomass recycling, providing priorities for future research.

microbiology↗

bioRxiv2020

Plankton Planet: 'seatizen' oceanography to assess open ocean life at the planetary scale

In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called plankton, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modelled at the planetary scale, but biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce Plankton Planet, an initiative whose goal is to merge the creativity of researchers, makers, and mariners to (i) develop frugal scientific instrumentation and protocols to assess the genetic and morphological diversity of plankton life, and (ii) organize their systematic deployment through fleets of volunteer sailors, fishermen, or cargo-ships to generate comparable and open-access plankton data across global and long-term spatio-temporal scales. As proof-of-concept, we show how 20 crews of sailors ("planktonauts") were abl to sample plankton biomass from the world surface ocean in a single year, generating the first citizen-based, planetary dataset of plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. This dataset has unveiled significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems across the dimensions of the Earth system.

ecology↗